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Switch out the API #37

Merged
merged 24 commits into from
Mar 1, 2024
Merged

Switch out the API #37

merged 24 commits into from
Mar 1, 2024

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MillironX
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Well, here it is: the big rewrite. I don't want this merged yet, but want it to be available for everyone to be testing against. Please try some of your biggest and baddest testing workflows against this branch (I've committed the sin of committing the build to the branch so we can do that).

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d44aa34..48b4c4c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
         uses: actions/checkout@v4

       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
         with:
           version: "${{ matrix.NXF_VER }}"

This is a breaking change, so I want to properly deprecate the unused parameters on v1 today, then move this to v2 once it's properly tested.

@MillironX
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MillironX commented Feb 9, 2024

Things that I want to see before merging this PR:

  • Confirmation of a successful stress-test from someone at @nf-core/modules
  • Confirmation of a successful stress-test from someone at @nf-core/sarek

I have personally stress-tested this PR on taxprofiler, since that pipeline is near and dear to me. I want someone else (who doesn't have a conflict of interest) to do their best to break it on some of our most problematic repos, though. Hopefully we can get this version into the template before the hackathon!

@mashehu
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mashehu commented Feb 9, 2024

For modules, I just kicked off this one again: https://github.com/nf-core/modules/pull/4726/checks, might be a good candidate

@MillironX
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For modules, I just kicked off this one again: nf-core/modules#4726 (checks), might be a good candidate

That one is still pointed at nf-core/setup-nextflow@v1. In order to test the new API, submit a pull request with MillironX/setup-nextflow@feature/api-switch. Just mark it as draft or something along those lines to make sure it doesn't get merged.

@mashehu
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mashehu commented Feb 9, 2024

Looking good for now: https://github.com/nf-core/modules/actions/runs/7845940111/job/21411506756

@MillironX
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All right, I'm giving @nf-core/sarek team one week before I merge and tag this. Otherwise I won't have time to get the pipeline template updated before the hackathon. Have fun!

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@MatthiasZepper MatthiasZepper left a comment

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Excellent work! Thanks a lot!

Minor remark: When I ran npm audit (v21.6.1/npm v10.2.4), it warned me about several security vulnerabilities in the dependencies, including a highly critical one in the JSON parsing. Although we trust the API in that case, I think it can't harm to run an npm audit fix and commit the updated package-lock.json.

Per @ewels request, the API on nf-co.re includes a "published_at" field
with the date of each release. For future compatibility without breaking
anything current, add an optional field that can handle this additional
information.
Basically, a stand-in for OctoKit, but smarter.
Although it seems like we're moving backwards, the new API only supports a
single data dump. I still like the iterative nature rather, so tack on
array support.
This functionality is now offloaded to the API.
…rsion

This is to preserve consistency with the new API
This is no longer needed under the new API.
@MillironX MillironX marked this pull request as ready for review March 1, 2024 00:58
@MillironX MillironX merged commit 0dada87 into nf-core:master Mar 1, 2024
16 checks passed
@MillironX MillironX deleted the feature/api-switch branch March 1, 2024 01:05
@MillironX MillironX mentioned this pull request Oct 3, 2024
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4 participants